Hello gromacs user
I am trying to calculate the various properties from the membrane simulation.
As I am trying to explore the various properties which I can calculate from the
trajectory using various module given in the gromacs.
But I felt difficulties in understanding the various output
Hi Debashis,
I haven't looked at your trajectory but I suspect this will answer your
question:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Cara
Date: Fri, 15 May 2015 12:02:31 +0530
From: debashis.sah...@gmail.com
To: gmx-us...@gromacs.org
Subject: Re:
During calculation of RMSD distribution using *g_cluster*, the Y axis of
the XVG file showing the RMSD distribution denotes a.u. i.e arbitrary unit
which I think probably the frequency. But it is not clear which frequency
it exactly is and also kindly let me know how the calculation happened.
--
Dear Justin,
I have decreased the box size than previous box case. Now
I have mentioned coupling between the system and the rest of mix solvent
and ion. The trajectory of the MD is better than the earlier in this new
box (water 345 and acetonitrile 48) cases. But there is a
Dear All,
can anyone send me the GROMACS Script file to run in
cluster.
Email id: sivanandam...@gmail.com
M.SIVANANDAM
Research Scholar
Department of Physics
Periyar University
Salem-636 011
Mobile- 9965582730, 9042066076
On 5/15/15 1:36 AM, Kashif wrote:
I have done MD simulation of my protein and ligand docked complex. My
protein is having 900 amino acids. When I use g_rms to analyse rmsd, the
graph is too short. Currently I am simulating my protein for 5 ns. Should I
increase my ns for such big protein and
On 5/14/15 10:02 PM, Ming Tang wrote:
Hi Justin
Here is the .mdp file with position restraints, which I downloaded from the
martini tutorial website. It works well with the tutorial and my small triple
helix, and the grompp process does not give any warnings. Please help to have a
look.
On 5/15/15 6:29 AM, sanjay choubey wrote:
HI, Thanks for your cooperation. Last time i asked about grompp error in
running membrane dynamics simulation. THe error was atom type CA Not found.
You suggested me to remove CA from DPPC.itp. But no effect still i am getting
I did not suggest
On 5/15/15 9:32 AM, Ming Tang wrote:
Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be
reasonable according to gromacs website. So ijust kept trying 0.02ps
The time step will depend on the stability of the system, which in turn depends
on how well equilibrated it is.
I'm so glad to tell that the question seemed to be solved after I refine the
charge of Zn atom and the atoms around it.
+2 may be too much for the Zn atom, and reduce the positive charge according
to the results of resp calculation.
Also I think the simulation could be further refined after
Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be
reasonable according to gromacs website. So ijust kept trying 0.02ps
Sent from my Huawei Mobile
Justin Lemkul jalem...@vt.edu wrote:
On 5/14/15 10:02 PM, Ming Tang wrote:
Hi Justin
Here is the .mdp file with position
On 5/15/15 4:15 PM, Ta-Chou 黃大周 wrote:
Dear all,
Actually, I had google for this error message, but I can't understand the
answer clearly, and it seems the previous question didn't finish yet.
I want to run a MD simulation with amber force field for a membrane protein.
And the simulation box
Hi,
I am not sure anyone will be able to help, because this isn't really about
Gromacs. Can you please clarify who they are and what exactly you mean by
perpendicular when talking about surfactants? Also, what are those
surfactants? Anyway, a reference to a representative paper and some
Golnaz,
I think you're creating a bit of a mess by replying to the digest. If
you don't mind, please see my answer directly to your specific
question, where I will also quote your message from below.
Alex
GR Thank you Alex
GR First of all it is better to say that I am a beginner. I follow two
Okay, I looked at the first paper. As Abhijit said, you can manipulate any part of your input coordinates by using something like packmol. In addition, pymol and GMX itself (editconf) provides means for translation and rotation of your choosing. I think VMD has this functionality as well,
Hi Justin,
Thanks for your email. I have modified it and the topology looks fine to me
or at least I can't see any problem with it but still genion does not like
it? Would please have a look?
https://drive.google.com/file/d/0B0YMTXH1gmQsSl9KbWhXaWJKc1k/view?usp=sharing
Dear all,
Actually, I had google for this error message, but I can't understand the
answer clearly, and it seems the previous question didn't finish yet.
I want to run a MD simulation with amber force field for a membrane protein.
And the simulation box contains my goal membrane protein, POPC
17 matches
Mail list logo